4YZY | pdb_00004yzy

Crystal structures reveal transient PERK luminal domain tetramerization in ER stress signaling

• PDB DOI: https://doi.org/10.2210/pdb4YZY/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-25 Released: 2015-05-13 
• Deposition Author(s): Carrara, M., Prischi, F., Ali, M.M.U.
• Funding Organization(s): Cancer Research UK, Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.305 (Depositor), 0.340 (DCC) 
• R-Value Work: 
  0.290 (Depositor), 0.342 (DCC) 
• R-Value Observed: 
  0.291 (Depositor) 

Starting Model: experimental

Literature

Crystal structures reveal transient PERK luminal domain tetramerization in endoplasmic reticulum stress signaling.

Carrara, M., Prischi, F., Nowak, P.R., Ali, M.M.

(2015) EMBO J 34: 1589-1600

• PubMed: 25925385 
• DOI: https://doi.org/10.15252/embj.201489183
• Primary Citation Related Structures: 
  4YZS, 4YZY


• PubMed Abstract: 
  

  Stress caused by accumulation of misfolded proteins within the endoplasmic reticulum (ER) elicits a cellular unfolded protein response (UPR) aimed at maintaining protein-folding capacity. PERK, a key upstream component, recognizes ER stress via its luminal sensor/transducer domain, but the molecular events that lead to UPR activation remain unclear. Here, we describe the crystal structures of mammalian PERK luminal domains captured in dimeric state as well as in a novel tetrameric state. Small angle X-ray scattering analysis (SAXS) supports the existence of both crystal structures also in solution. The salient feature of the tetramer interface, a helix swapped between dimers, implies transient association. Moreover, interface mutations that disrupt tetramer formation in vitro reduce phosphorylation of PERK and its target eIF2α in cells. These results suggest that transient conversion from dimeric to tetrameric state may be a key regulatory step in UPR activation.

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Organizational Affiliation: 
• Department of Life Sciences, Imperial College, London, UK.
Department of Life Sciences, Imperial College, London, UK [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.51 kDa 
• Atom Count: 1,186 
• Modeled Residue Count: 163 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2-alpha kinase 3	A	301	Mus musculus	Mutation(s): 0  Gene Names: Eif2ak3, Pek, Perk EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt
Find proteins for Q9Z2B5 (Mus musculus) Explore Q9Z2B5  Go to UniProtKB:  Q9Z2B5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.305 (Depositor), 0.340 (DCC) 
• R-Value Work:  0.290 (Depositor), 0.342 (DCC) 
• R-Value Observed: 0.291 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.77	α = 90
b = 90.77	β = 90
c = 75.22	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
SCALA	data scaling
Coot	model building
MOSFLM	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Carrara, M., Prischi, F., Ali, M.M.U.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C33269/A11161
Medical Research Council (United Kingdom)	United Kingdom	MR/L007436/1

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2015-06-17
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary